Table 1. Comparison of pipeline functionality of common ancient DNA processing pipelines.

Category	Functionality	EAGER	PALEOMIX	nf-core/eager
Infrastructure	Software environments	Yes	No	Yes
	HPC scheduler integration	No	No	Yes
	Cloud computing integration	No	No	Yes
	Per-process resource optimisation	No	Partial	Yes
	Pipeline-step parallelisation	No	Yes	Yes
	Command line set up	No	Yes	Yes
	GUI set up	Yes	No	Yes
Preprocessing	Sequencing lane merging	Yes	Yes	Yes
	Sequencing quality control	Yes	No	Yes
	Sequencing artefact removal	No	No	Yes
	Adapter clipping/read merging	Yes	Yes	Yes
	Post-processing sequencing QC	No	No	Yes
Alignment	Reference mapping	Yes	Yes	Yes
	Reference mapping statistics	Yes	Yes	Yes
	Multi-reference mapping	No	Yes	No
Postprocessing	Mapped reads filtering	Yes	Yes	Yes
	Metagenomic complexity filtering	No	No	Yes
	Metagenomic profiling	No	No	Yes
	Metagenomic authentication	No	No	Yes
	Library complexity estimation	Yes	No	Yes
	Duplicate removal	Yes	No	Yes
	BAM merging	No	Yes	Yes
Authentication	Damage read filtering	Yes	No	Yes
	Human contamination estimation	Yes	No	Yes
	Human biological sex determination	No	No	Yes
	Genome coverage estimation	Yes	Yes	Yes
	Damage calculation	Yes	Yes	Yes
	Damage rescaling	No	Yes	Yes
Downstream	SNP calling/genotyping	Yes	Partial	Yes
	Consensus sequence generation	Yes	Partial	Yes
	Regions of interest statistics	Partial	Yes	Yes